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Commander Shepard first encounters Legion after the Illusive Man sends him to recover the IFF onboard a Derelict Reaper. As Shepard progress through the Reaper's interior, he is met with heavy resistance from a Cerberus investigation team that have succumbed to the Reaper's still active indoctrination affects. The indoctrination has changed the team into mindless husks. Further into the Reaper's interior, Shepard becomes surrounded by a group of Husks. It is here in which Legion reveals himself, surprised to see Shepard alive. The Geth refers to him as Shepard-Commander, before using his Sniper Rifle to assist Shepard in killing the Husks. As Shepard approaches the Reaper's mass effect core, Legion is again encountered. Legion attempts to using a Terminal to remove the shields blocking Shepard's path. As it does so, it is attacked by numerous Husks, one of which disables Legion. After destroying the Reaper's core, Shepard decides to take the Geth back to the Normandy. Shepard must then choose to activate the Geth or give it to Cerberus for research. If given to Cerberus, Shepard will receive 50,000 credits as intact Geth are difficult to recover. Alternatively, Shepard can activate the Geth. If Shepard wishes to interact the Geth, it can be found lying in the Normandy's AI Core, under guard from one of the Cerberus Soldiers onboard. Here, Shepard can reactivate the Geth, who will then join your squad. When asked for its name, the machine will simply reply "Geth". Shepard repeats the question, until EDI suggests a name from a passage in the New Testament. EDI then submits a quote from Mark 5:9 - "My name is Legion, for we are many." The Geth believes this to be an "appropriate metaphor" and is then referred to as Legion.

Legion is a unique Geth unit, in that it is designed to operate outside the Perseus Veil and interact directly with organics. To help it preform its operations, Legion contains 1,183 different Geth programs, as opposed to the usual 100 or so in normal Geth units. This is to help Legion communicate with organics and act independently from other Geth unit, not needing to rely on the Geth neural network for its intelligence. After its creation, Legion was tasked with investigating the destruction of the "Old Machine" Nazara, which the galaxy knew as the ReaperSovereign. Legion then retraced Shepard's step, revisiting several of the different planets Shepard visited - Eden Prime, Therum, Feros, Noveria, Virmire, Ilos and a dozen uncharted worlds. While investigating Eden Prime, Legion was attacked by Alliance soldiers, one of which blew a hole in its chest. Eventually Legion found the remains of the Normandy crash site on the planet Alchera. While investigating the crash site, Legion found pieces of Shepard's N7 armor. It then incorporated the armor into itself to repair damage sustained on Eden Prime. Legion is unwilling to say why it waited so long to repair itself or why it used specifically chose Shepard's armor, claiming, "There was a hole". When pressed on the subject, Legion will claim, "No data available".

Legion is able to express more human emotions that a machine typically would. The panels on Legion's head are used in the same purpose as humans do with their eyes and eyebrows. Legion is able to move these panels to represent various emotions, such as; raising to imply surprise or interest and folding forward to show concentration. It uses these panels in combination with the light emitting from its head to show anger and generally positive emotions. As Legion consists of 1,183 Geth programs, it has a higher Artificial Intelligence than other Geth. This results in Legion being able to speak in constructive and detailed sentences. Its voice is straight-forward and in a synthetic fashion. Legion regards itself not as a single being, but as an A.I. platform, and consistently refers to itself as "we". Shepard and the rest of the squad refer to Legion as "it". When conversing with Legion about the fate of the "Heretic Geth" following the completion of his Loyalty mission, Legion will say, "...I could review all my time on the Normandy...". This may show that Legion is beginning to understand and accept the idea of individualism.

After the completion of the Suicide Mission, providing Legion survived he will share his thoughts on the outcome. Legion will show surprise that Shepard destroyed the Human-Reaper, claiming that the Reaper represents everything the Geth wish, "unity, transcendence". If Shepard destroyed the Collector Base, Legion will compare it to the "True Geth" refusing to help the Reapers in exchange for their technology, commenting "perhaps you are not so different from us". If Shepard keeps the Collector Base intact, Legion will recommend not using it, believing that organics have great potential and sure achieve greatness independently, like the "True Geth".